# HG changeset patch # User lecorguille # Date 1461597242 14400 # Node ID 451ff602a957b1874ca4437f0bc872635ce94a55 # Parent 0888f7ef739a75af7e5519812b2921918a1a555f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 diff -r 0888f7ef739a -r 451ff602a957 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Fri Apr 08 10:38:52 2016 -0400 +++ b/abims_xcms_xcmsSet.xml Mon Apr 25 11:14:02 2016 -0400 @@ -183,7 +183,7 @@ - + + + + + + + + + + + + + + + + + diff -r 0888f7ef739a -r 451ff602a957 planemo_test.sh --- a/planemo_test.sh Fri Apr 08 10:38:52 2016 -0400 +++ b/planemo_test.sh Mon Apr 25 11:14:02 2016 -0400 @@ -1,18 +1,33 @@ -planemo conda_init -planemo conda_install . -planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" +# Example of planemo command to launch test + +# Note: --galaxy_branch "dev" is set to deal with zip file + + +# -- Use of installed package environments +# after having installing package on a local galaxy instance +source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh +source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh +planemo test --install_galaxy --galaxy_branch "dev" #All 2 test(s) executed passed. #abims_xcms_xcmsSet[0]: passed #abims_xcms_xcmsSet[1]: passed - - -source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh -source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh -planemo test --install_galaxy --galaxy_branch "dev" +# -- Use of conda dependencies +planemo conda_init --conda_prefix /tmp/mc +planemo conda_install --conda_prefix /tmp/mc . +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" #All 2 test(s) executed passed. #abims_xcms_xcmsSet[0]: passed -#abims_xcms_xcmsSet[1]: passed \ No newline at end of file +#abims_xcms_xcmsSet[1]: passed + + +# -- Use of shed_test +planemo shed_test --install_galaxy -t testtoolshed --galaxy_branch ="dev" + +#All 2 test(s) executed passed. +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[0]: passed +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_xcmsset/2.0.8[1]: passed + diff -r 0888f7ef739a -r 451ff602a957 test-data/faahKO_reduce.zip Binary file test-data/faahKO_reduce.zip has changed diff -r 0888f7ef739a -r 451ff602a957 test-data/sacuri_current_root.zip Binary file test-data/sacuri_current_root.zip has changed diff -r 0888f7ef739a -r 451ff602a957 test-data/sacuri_dir_root.log.txt --- a/test-data/sacuri_dir_root.log.txt Fri Apr 08 10:38:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ - PACKAGE INFO -parallel 3.2.2 -BiocGenerics 0.16.1 -Biobase 2.30.0 -Rcpp 0.12.2 -mzR 2.4.1 -xcms 1.44.0 -snow 0.4.1 -batch 1.1.4 - - - ARGUMENTS INFO -zipfile /tmp/tmpAmhDSv/files/000/dataset_1.dat -xfunction xcmsSet -xsetRdataOutput /tmp/tmpAmhDSv/files/000/dataset_2.dat -sampleMetadataOutput /tmp/tmpAmhDSv/files/000/dataset_3.dat -ticspdf /tmp/tmpAmhDSv/files/000/dataset_4.dat -bicspdf /tmp/tmpAmhDSv/files/000/dataset_5.dat -nSlaves 1 -method matchedFilter -step 0.01 -fwhm 4 -max 50 -snthresh 1 -steps 2 - - - INFILE PROCESSING INFO - - - ARGUMENTS PROCESSING INFO -files_root_directory sacuri -Compute md5 checksum... -Checking XML structure... -Checking files filenames compatibilities with xmcs... - - - MAIN PROCESSING INFO -55:579 60:1264 65:1988 70:2602 75:3287 80:3894 85:4629 90:5499 95:6174 100:6672 105:7194 110:7737 115:8205 120:8673 125:9117 130:9532 135:9973 140:10562 145:10945 150:11380 155:11788 160:12163 165:12477 170:12835 175:13276 180:13632 185:14142 190:14489 195:15022 200:15360 205:15716 210:15992 215:16297 220:16669 225:16895 230:17227 235:17487 240:17657 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935:26339 940:26356 945:26367 950:26381 955:26392 960:26404 965:26592 970:26701 975:26720 980:26743 985:26759 990:26969 995:26990 - - -null device - 1 -Creating the sampleMetadata file... -Creating TIC pdf... -Creating BIC pdf... - - - XSET OBJECT INFO -An "xcmsSet" object with 4 samples - -Time range: 0.7-1139.7 seconds (0-19 minutes) -Mass range: 50.0021-999.9863 m/z -Peaks: 59359 (about 14840 per sample) -Peak Groups: 0 -Sample classes: bio, blank - -Profile settings: method = bin - step = 0.01 - -Memory usage: 6.02 MB - - - DONE diff -r 0888f7ef739a -r 451ff602a957 test-data/sacuri_dir_root.zip Binary file test-data/sacuri_dir_root.zip has changed